Hi Kevin- 

That's truly odd. The error happens when the offending file is imported, which 
means that 
it is a syntax issue that should have been seen earlier. I'll take a look at 
this soon (unless someone 
else beats me to it). 

In the meantime, of course, do not use the use_tasked_jobs on this instance of 
Galaxy. If others 
have seen similar issues, then please speak up. 

-Scott 

----- Original Message -----

> Hi,

> I am using Python 2.7. I am running with an hg checked out, up to
> date version of " https://bitbucket.org/galaxy/galaxy-dist/ ".

> I am very new to Galaxy. I have an instance setup and running
> locally. I am able to perform routine actions such as uploading
> files, processing with Picard, and aligning with BWA. I have been
> able to make the jobs execute out our SGE cluster.

> In order to better utilize my cluster, I attempted to enable
> parallelism of the tasks that support it (such as BWA) by
> configuring the universe_wsgi.ini file with the parameter

> use_tasked_jobs = True

> When I do this and attempt execute a BWA alignment on a 4.1Gb fastq
> file, I am given the error

> > Result 256 from mv
> > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat
> > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat
> 
> > /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0:
> 
> > Traceback (most recent call last):
> 
> > File "./scripts/extract_dataset_part.py", line 25, in ?
> 
> > import galaxy.model.mapping #need to load this before we unpickle,
> > in
> > order to setup properties assigned by the mappers
> 
> > File
> > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py",
> > line 13, in ?
> 
> > import galaxy.datatypes.registry
> 
> > File
> > "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py",
> > line 146
> 
> > finally:
> 
> > ^
> 
> > SyntaxError: invalid syntax
> 
> > The alignment failed.
> 
> If you need the complete error message, contact me and I can supply
> you with it. It's too large to paste in-line and attachments aren't
> allowed.

> Is there more I need to do to enable parallel jobs (splitting of
> input, align, then merge)?

> Any suggestions are greatly appreciated.

> Kevin
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___________________________________________________________
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